How many miles should I put on the stock setup before I ad the ap and amaybe do the twin scroll setup?

At least break-in the car for 1000 miles, before you start modding. Start with the usual USDM bolt-on stuff if you aren't sure about how much you want to push. You might be satisfied and stop there. If you aren't then consider the twin-scroll. By itself the twin-scroll doesn't make a ton more power, just allows you to have better spool-up while still increasing power potential. You can get great spool-up on an uprated standard turbo if you select your parts carefully and do some port work on the manifolds, head and turbo.